Dear Matt, Thank you for the quick response. The first error gets indeed resolved by removing the atoms labeled with a B. I was not very clear in my first post that I had to do this to have the ATOMS window run properly in Artemis. The problem I am stuck on is that when I have them removed and then run the FEFF window, it seems to all work fine, until I try and drag the paths into the Path window in Artemis. At that point the paths seem to no longer exist.
I hope this clears up my question a bit more. Kind regards, Anouk On Thu, May 25, 2023 at 7:02 PM <ifeffit-requ...@millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit@millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-requ...@millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-ow...@millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Problems with FEFF calculation using CIF file (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 24 May 2023 12:29:01 -0500 > From: Matt Newville <newvi...@cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Problems with FEFF calculation using CIF file > Message-ID: > <CA+7ESbpH97zi+-xbK2R62m8ND-MG+6OgMB= > r16zsqxe2za7...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Anouk, > > I am not sure what is happening with that CIF file. When I try to read > that with pymatgen, I get > > >>> from pymatgen.io.cif import CifParser > >>> structs = CifParser('VOXZAJ.cif') > >>> structs.get_structures() > .../site-packages/pymatgen/io/cif.py:1145: UserWarning: Error is Species > occupancies sum to more than 1!. > warnings.warn(f"Error is {str(exc)}.") > .../site-packages/pymatgen/io/cif.py:1148: UserWarning: Issues encountered > while parsing CIF: Some occupancies ([2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, > 2, 2, 2, 2, 2, 2, 2, 2]) sum to > 1! If they are within the > occupancy_tolerance, they will be rescaled. The current occupancy_tolerance > is set to: 1.0 > Species occupancies sum to more than 1! > warnings.warn("Issues encountered while parsing CIF: " + > "\n".join(self.warnings)) > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > .../site-packages/pymatgen/io/cif.py", line 1150, in get_structures > raise ValueError("Invalid cif file with no structures!") > ValueError: Invalid cif file with no structures! > > If you remove all the atomic sites that have a "B" in their name, that gets > resolved, but I do not know if that is still the correct structure - or > what the "B" means. > > CIF is complicated, but just from a practical point of view, I think we are > going to take `pymatgen` as the arbitrator of "valid CIF". > > > On Wed, May 24, 2023 at 11:30?AM Volker, Anouk <a.vol...@student.rug.nl> > wrote: > > > Dear all, > > > > I hope this email finds you well. I have encountered a problem that I > have > > not been able to fix on my own. I have a specific CIF file (from the > CCDC > > database) that is attached to the e-mail. After removing the duplicate > > atoms in the file, the ATOMS window seems fine. The FEFF calculation will > > run without any errors and within the FEFF window the paths are displayed > > and can be plotted. The problem arises when I try to take some of the > paths > > from the FEFF window and drag them into the Path window. Now the paths > can > > no longer be plotted and when trying to use them to fit, it seems like > the > > paths are non-existent as well. > > > > Is there something wrong with the CIF file that causes this to happen and > > if so, what can be done to fix it? I have already tried to make a > feff.inp > > file from the xyz data (after opening the CIF file in any viewer), but > this > > gives the same problem. > > > > Thank you in advance, > > > > Kind regards, > > Anouk Volker > > > > Master student, Browne Group > > Stratingh Institute, University of Groningen > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit@millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > > -- > --Matt Newville <newville at cars.uchicago.edu> 630-327-7411 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20230524/90ae40d2/attachment-0001.htm > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > ------------------------------ > > End of Ifeffit Digest, Vol 243, Issue 17 > **************************************** >
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